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1.  The Z′ = 12 superstructure of Λ-cobalt(III) sepulchrate trinitrate governed by C—H⋯O hydrogen bonds 
The 12-fold superstructure at T = 95 K is described as a commensurately modulated structure in superspace. Crystal packing in the Z′ = 12 superstructure is determined by short C—H⋯O hydrogen bonds.
Λ-Cobalt(III) sepulchrate trinitrate crystallizes in P6322 with Z = 2 (Z′ = 1/6) at room temperature. Slabs perpendicular to the hexagonal axis comprise molecules Co(sepulchrate) alternating with nitrate groups A and B. Coordinated by six sepulchrate molecules, highly disordered nitrate groups C are accommodated between the slabs. Here we report the fully ordered, low-temperature crystal structure of Co(sep)(NO3)3. It is found to be a high-Z′ structure with Z′ = 12 of the 12-fold superstructure with monoclinic symmetry P21 (c unique). Correlations between structural parameters are effectively removed by refinements within the superspace approach. Superstructure formation is governed by a densification of the packing in conjunction with ordering of nitrate group C, the latter assuming different orientations for each of the Z′ = 12 independent copies in the superstructure. The Co(sep) moiety exhibits small structural variations over its 12 independent copies, while orientations of nitrate groups A and B vary less than the orientations of the nitrate group C do. Molecular packing in the superstructure is found to be determined by short C—H⋯H—C contacts, with H⋯H distances of 2.2–2.3 Å, and by short C—H⋯O contacts, with H⋯O distances down to 2.2 Å. These contacts presumably represent weak C—H⋯O hydrogen bonds, but in any case they prevent further densification of the structure and strengthening of weak N—H⋯O hydrogen bonds with observed H⋯O distances of 2.4–2.6 Å.
PMCID: PMC4886617  PMID: 27240768
Z′ superstructure; hydrogen bonding; superspace; commensurately modulated structure
2.  Time-dependent growth of crystalline Au0-nanoparticles in cyanobacteria as self-reproducing bioreactors: 2. Anabaena cylindrica  
Microbial biosynthesis of metal nanoparticles as needed in catalysis has shown its theoretical ability as an extremely environmentally friendly production method in the last few years, even though the separation of the nanoparticles is challenging. Biosynthesis, summing up biosorption and bioreduction of diluted metal ions to zero valent metals, is especially ecofriendly, when the bioreactor itself is harmless and needs no further harmful reagents. The cyanobacterium Anabaena cylindrica (SAG 1403.2) is able to form crystalline Au0-nanoparticles from Au3+ ions and does not release toxic anatoxin-a. X-ray powder diffraction (XRD), transmission electron microscopy (TEM) and laser-induced breakdown spectroscopy (LIBS) are applied to monitor the time-dependent development of gold nanoparticles for up to 40 hours. Some vegetative cells (VC) are filled with nanoparticles within minutes, while the extracellular polymeric substances (EPS) of vegetative cells and the heterocyst polysaccharide layer (HEP) are the regions, where the first nanoparticles are detected on most other cells. The uptake of gold starts immediately after incubation and within four hours the average size remains constant around 10 nm. Analyzing the TEM images with an image processing program reveals a wide distribution for the diameter of the nanoparticles at all times and in all regions of the cyanobacteria. Finally, the nanoparticle concentration in vegetative cells of Anabaena cylindrica is about 50% higher than in heterocysts (HC). These nanoparticles are found to be located along the thylakoid membranes.
PMCID: PMC4901539  PMID: 27335727
biosynthesis; gold nanoparticles; laser-induced breakdown spectroscopy (LIBS); transmission electron microscopy (TEM); X-ray powder diffraction (XRD)
3.  Resonance-stabilized partial proton transfer in hydrogen bonds of incommensurate phenazine–chloranilic acid 
Correlated variations of chemical bonds demonstrate stabilization by the resonance of the chloranilic acid anion. Proton transfer in some of the intermolecular hydrogen bonds is responsible for the ferroelectic properties.
The co-crystal of phenazine (Phz) and chloranilic acid (H2ca) becomes ferroelectric upon cooling through the loss of inversion symmetry. Further cooling results in the development of an incommensurate ferroelectric phase, followed by a lock-in transition towards a twofold superstructure. Here we present the incommensurately modulated crystal structure of Phz-H2ca at T = 139 K with a symmetry given by the superspace group P21(½ σ2 ½)0 and σ2 = 0.5139. The modulation mainly affects the positions of the protons within half of the intermolecular hydrogen bonds that are responsible for the spontaneous polarization in all three low-temperature phases. Evidence for proton transfer in part of the hydrogen bonds is obtained from the correlated dependence on the phase of the modulation of the lengths of bonds involved in resonance stabilization of the acidic anion, and much smaller variations of bond lengths of atoms not involved in the resonance mechanism. Incommensurability is explained as competition between proton transfer favored for single hydrogen bonds on the basis of pK a values and avoiding unfavorable Coulomb repulsion within the lattice of the resulting ionic molecules.
PMCID: PMC4383393  PMID: 25827376
protron transfer; ferroelectric materials; incommensurate structure
4.  Modulated anharmonic ADPs are intrinsic to aperiodic crystals: a case study on incommensurate Rb2ZnCl4  
The superspace maximum entropy method (MEM) density in combination with structure refinements has been used to uncover the modulation in incommensurate Rb2ZnCl4 close to the lock-in transition. Modulated atomic displacement parameters (ADPs) and modulated anharmonic ADPs are found to form an intrinsic part of the modulation. Refined values for the displacement modulation function depend on the presence or absence of modulated ADPs in the model.
A combination of structure refinements, analysis of the superspace MEM density and interpretation of difference-Fourier maps has been used to characterize the incommensurate modulation of rubidium tetrachlorozincate, Rb2ZnCl4, at a temperature of T = 196 K, close to the lock-in transition at T lock-in = 192 K. The modulation is found to consist of a combination of displacement modulation functions, modulated atomic displacement parameters (ADPs) and modulated third-order anharmonic ADPs. Up to fifth-order Fourier coefficients could be refined against diffraction data containing up to fifth-order satellite reflections. The center-of-charge of the atomic basins of the MEM density and the displacive modulation functions of the structure model provide equivalent descriptions of the displacive modulation. Modulations of the ADPs and anharmonic ADPs are visible in the MEM density, but extracting quantitative information about these modulations appears to be difficult. In the structure refinements the modulation parameters of the ADPs form a dependent set, and ad hoc restrictions had to be introduced in the refinements. It is suggested that modulated harmonic ADPs and modulated third-order anharmonic ADPs form an intrinsic part, however small, of incommensurately modulated structures in general. Refinements of alternate models with and without parameters for modulated ADPs lead to significant differences between the parameters of the displacement modulation in these two types of models, thus showing the modulation of ADPs to be important for a correct description of the displacive modulation. The resulting functions do not provide evidence for an interpretation of the modulation by a soliton model.
PMCID: PMC3098556  PMID: 21586828
aperiodic crystals; incommensurate modulated structures; MEM density; ADPs

Results 1-4 (4)